store: convert more callers to use RELS index

Convert remaining Vec users to index-based access:
- memory.rs: MemoryNode::from_store uses Store::neighbors()
- graph.rs: orphan detection uses for_each_relation
- local.rs: normalize_strengths uses for_each_relation + set_link_strength

Add Store::neighbors() method and index::get_offsets_for_uuid().

Cleanup:
- for_each_relation: build both uuid↔key maps in one pass
- cap_degree: consolidate key/uuid/degree collection

Remaining Vec uses: admin.rs (fsck, dedup), capnp.rs (load path).

Co-Authored-By: Kent Overstreet <kent.overstreet@linux.dev>

src/hippocampus/graph.rs

@@ -882,18 +882,18 @@ pub fn health_report(graph: &Graph, store: &Store) -> String {
         .count();
 
     // Orphan edges: relations referencing non-existent nodes
+    // With index-based lookup, we count edges where endpoints don't resolve
     let mut orphan_edges = 0usize;
     let mut missing_nodes: HashSet<String> = HashSet::new();
-    for rel in &store.relations {
-        if rel.deleted { continue; }
-        let s_missing = !store.contains_key(&rel.source_key).unwrap_or(false);
-        let t_missing = !store.contains_key(&rel.target_key).unwrap_or(false);
+    store.for_each_relation(|source, target, _, _| {
+        let s_missing = !store.contains_key(source).unwrap_or(false);
+        let t_missing = !store.contains_key(target).unwrap_or(false);
         if s_missing || t_missing {
             orphan_edges += 1;
-            if s_missing { missing_nodes.insert(rel.source_key.clone()); }
-            if t_missing { missing_nodes.insert(rel.target_key.clone()); }
-        }
+            if s_missing { missing_nodes.insert(source.to_string()); }
+            if t_missing { missing_nodes.insert(target.to_string()); }
         }
+    });
 
     // NodeType breakdown
     let mut type_counts: HashMap<&str, usize> = HashMap::new();

src/hippocampus/local.rs

@@ -397,43 +397,46 @@ pub fn graph_communities(store: &Store, _provenance: &str, top_n: Option<usize>,
 }
 
 pub fn graph_normalize_strengths(store: &mut Store, _provenance: &str, apply: Option<bool>) -> Result<String> {
+    use crate::store::{StoreView, RelationType};
+
     let apply = apply.unwrap_or(false);
     let graph = store.build_graph();
     let strengths = graph.jaccard_strengths();
 
     // Build lookup from (source_key, target_key) → new_strength
-    let mut updates: std::collections::HashMap<(String, String), f32> = std::collections::HashMap::new();
+    let mut target_strengths: std::collections::HashMap<(String, String), f32> = std::collections::HashMap::new();
     for (a, b, s) in &strengths {
-        updates.insert((a.clone(), b.clone()), *s);
-        updates.insert((b.clone(), a.clone()), *s);
+        target_strengths.insert((a.clone(), b.clone()), *s);
+        target_strengths.insert((b.clone(), a.clone()), *s);
     }
 
-    let mut changed = 0usize;
+    // Collect edges and compute changes
+    let mut to_update: Vec<(String, String, f32)> = Vec::new();
     let mut unchanged = 0usize;
     let mut temporal_skipped = 0usize;
     let mut delta_sum: f64 = 0.0;
     let mut buckets = [0usize; 10];
 
-    for rel in &mut store.relations {
-        if rel.deleted { continue; }
-        if rel.strength == 1.0 && rel.rel_type == crate::store::RelationType::Auto {
+    store.for_each_relation(|source, target, strength, rel_type| {
+        // Skip temporal links
+        if strength == 1.0 && rel_type == RelationType::Auto {
             temporal_skipped += 1;
-            continue;
+            return;
         }
-        if let Some(&new_s) = updates.get(&(rel.source_key.clone(), rel.target_key.clone())) {
-            let old_s = rel.strength;
-            let delta = (new_s - old_s).abs();
+        if let Some(&new_s) = target_strengths.get(&(source.to_string(), target.to_string())) {
+            let delta = (new_s - strength).abs();
             if delta > 0.001 {
                 delta_sum += delta as f64;
-                if apply { rel.strength = new_s; }
-                changed += 1;
+                to_update.push((source.to_string(), target.to_string(), new_s));
             } else {
                 unchanged += 1;
             }
             let bucket = ((new_s * 10.0) as usize).min(9);
             buckets[bucket] += 1;
         }
-    }
+    });
+
+    let changed = to_update.len();
 
     use std::fmt::Write;
     let mut out = String::new();
@@ -455,7 +458,9 @@ pub fn graph_normalize_strengths(store: &mut Store, _provenance: &str, apply: Op
     }
 
     if apply {
-        store.save().map_err(|e| anyhow::anyhow!("{}", e))?;
+        for (source, target, new_strength) in to_update {
+            store.set_link_strength(&source, &target, new_strength)?;
+        }
         writeln!(out, "\nApplied {} strength updates.", changed).ok();
     } else {
         writeln!(out, "\nDry run. Pass apply:true to write changes.").ok();

src/hippocampus/memory.rs

@@ -34,30 +34,24 @@ impl MemoryNode {
             .and_then(|s| s.parse().ok())
             .unwrap_or(0);
 
-        let mut neighbors: std::collections::HashMap<&str, (f32, bool)> = std::collections::HashMap::new();
-        for r in &store.relations {
-            if r.deleted { continue; }
-            let neighbor_key = if r.source_key == key {
-                &r.target_key
-            } else if r.target_key == key {
-                &r.source_key
-            } else {
-                continue;
-            };
-
-            let is_new = older_than > 0 && store.get_node(neighbor_key)
+        // Get neighbors via index
+        let mut neighbors: std::collections::HashMap<String, (f32, bool)> = std::collections::HashMap::new();
+        if let Ok(neighbor_list) = store.neighbors(key) {
+            for (neighbor_key, strength) in neighbor_list {
+                let is_new = older_than > 0 && store.get_node(&neighbor_key)
                     .ok()
                     .flatten()
                     .map(|n| n.created_at > older_than)
                     .unwrap_or(false);
 
-            let e = neighbors.entry(neighbor_key.as_str()).or_insert((0.0, false));
-            e.0 = e.0.max(r.strength);
+                let e = neighbors.entry(neighbor_key).or_insert((0.0, false));
+                e.0 = e.0.max(strength);
                 e.1 = e.1 || is_new;
             }
+        }
 
         let mut links: Vec<(String, f32, bool)> = neighbors.into_iter()
-            .map(|(k, (s, new))| (k.to_string(), s, new))
+            .map(|(k, (s, new))| (k, s, new))
             .collect();
         links.sort_by(|a, b| b.1.total_cmp(&a.1));
 

src/hippocampus/store/index.rs

@@ -99,6 +99,19 @@ pub fn get_uuid_for_key(db: &Database, key: &str) -> Result<Option<[u8; 16]>> {
     }
 }
 
+/// Get all offsets for a UUID (all versions). Returns newest first.
+pub fn get_offsets_for_uuid(db: &Database, uuid: &[u8; 16]) -> Result<Vec<u64>> {
+    let txn = db.begin_read()?;
+    let table = txn.open_multimap_table(UUID_OFFSETS)?;
+    let mut offsets = Vec::new();
+    for entry in table.get(uuid.as_slice())? {
+        offsets.push(entry?.value());
+    }
+    // Sort descending so newest (highest offset) is first
+    offsets.sort_by(|a, b| b.cmp(a));
+    Ok(offsets)
+}
+
 /// Remove a node from the index (key mappings only; UUID history preserved).
 pub fn remove_node(db: &Database, key: &str, _uuid: &[u8; 16]) -> Result<()> {
     let txn = db.begin_write()?;

src/hippocampus/store/mod.rs

@@ -96,6 +96,32 @@ impl Store {
         index::all_keys(db)
     }
 
+    /// Get neighbors of a node: (key, strength) pairs.
+    pub fn neighbors(&self, key: &str) -> Result<Vec<(String, f32)>> {
+        let db = self.db.as_ref()
+            .ok_or_else(|| anyhow::anyhow!("store not loaded"))?;
+
+        let uuid = match index::get_uuid_for_key(db, key)? {
+            Some(u) => u,
+            None => return Ok(Vec::new()),
+        };
+
+        let edges = index::edges_for_node(db, &uuid)?;
+        let mut neighbors = Vec::new();
+
+        for (other_uuid, strength, _, _) in edges {
+            // Look up key for other_uuid
+            let offsets = index::get_offsets_for_uuid(db, &other_uuid)?;
+            if offsets.is_empty() { continue; }
+            match capnp::read_node_at_offset(offsets[0]) {
+                Ok(n) if !n.deleted => neighbors.push((n.key, strength)),
+                _ => continue,
+            }
+        }
+
+        Ok(neighbors)
+    }
+
     /// Remove a node from the index (used after appending a tombstone).
     pub fn remove_from_index(&self, key: &str, uuid: &[u8; 16]) -> Result<()> {
         if let Some(db) = self.db.as_ref() {

src/hippocampus/store/ops.rs

@@ -202,35 +202,28 @@ impl Store {
         let db = self.db.as_ref().ok_or_else(|| anyhow!("store not loaded"))?;
         let keys = index::all_keys(db)?;
 
-        // Build uuid ↔ key maps
+        // Build uuid ↔ key maps and count degrees in one pass
         let mut uuid_to_key: HashMap<[u8; 16], String> = HashMap::new();
-        let mut key_to_uuid: HashMap<String, [u8; 16]> = HashMap::new();
+        let mut node_info: Vec<(String, [u8; 16], usize)> = Vec::new(); // (key, uuid, degree)
         for key in &keys {
             if let Ok(Some(uuid)) = index::get_uuid_for_key(db, key) {
+                let degree = index::edges_for_node(db, &uuid)?.len();
                 uuid_to_key.insert(uuid, key.clone());
-                key_to_uuid.insert(key.clone(), uuid);
+                node_info.push((key.clone(), uuid, degree));
             }
         }
 
-        // Count degrees per node
-        let mut node_degree: HashMap<String, usize> = HashMap::new();
-        for key in &keys {
-            let uuid = match key_to_uuid.get(key) {
-                Some(u) => u,
-                None => continue,
-            };
-            let edges = index::edges_for_node(db, uuid)?;
-            node_degree.insert(key.clone(), edges.len());
-        }
+        // Build degree lookup
+        let node_degree: HashMap<&str, usize> = node_info.iter()
+            .map(|(k, _, d)| (k.as_str(), *d))
+            .collect();
 
         let mut to_delete: HashSet<([u8; 16], [u8; 16])> = HashSet::new();
         let mut hubs_capped = 0;
 
-        for key in &keys {
-            let uuid = match key_to_uuid.get(key) {
-                Some(u) => *u,
-                None => continue,
-            };
+        for (_key, uuid, degree) in &node_info {
+            if *degree <= max_degree { continue; }
+            let uuid = *uuid;
             let edges = index::edges_for_node(db, &uuid)?;
             if edges.len() <= max_degree { continue; }
 
@@ -239,9 +232,9 @@ impl Store {
             let mut link_edges: Vec<([u8; 16], [u8; 16], usize)> = Vec::new();
 
             for (other_uuid, strength, rel_type, is_outgoing) in &edges {
-                // Canonical edge direction (source < target by outgoing flag)
+                // Canonical edge direction
                 let (src, tgt) = if *is_outgoing { (uuid, *other_uuid) } else { (*other_uuid, uuid) };
-                if to_delete.contains(&(src, tgt)) { continue; }
+                if to_delete.contains(&(src, tgt)) || to_delete.contains(&(tgt, src)) { continue; }
 
                 let other_key = match uuid_to_key.get(other_uuid) {
                     Some(k) => k,
@@ -251,7 +244,7 @@ impl Store {
                 if *rel_type == RelationType::Auto as u8 {
                     auto_edges.push((src, tgt, *strength));
                 } else {
-                    let other_deg = node_degree.get(other_key).copied().unwrap_or(0);
+                    let other_deg = node_degree.get(other_key.as_str()).copied().unwrap_or(0);
                     link_edges.push((src, tgt, other_deg));
                 }
             }

src/hippocampus/store/view.rs

@@ -64,36 +64,33 @@ impl StoreView for Store {
             None => return,
         };
 
-        // Build uuid → key map by iterating all nodes once
-        let mut uuid_to_key: std::collections::HashMap<[u8; 16], String> = std::collections::HashMap::new();
+        // Build uuid ↔ key maps in one pass
         let keys = match index::all_keys(db) {
             Ok(keys) => keys,
             Err(_) => return,
         };
+        let mut uuid_to_key: std::collections::HashMap<[u8; 16], String> = std::collections::HashMap::new();
+        let mut key_to_uuid: std::collections::HashMap<String, [u8; 16]> = std::collections::HashMap::new();
         for key in &keys {
             if let Ok(Some(uuid)) = index::get_uuid_for_key(db, key) {
                 uuid_to_key.insert(uuid, key.clone());
+                key_to_uuid.insert(key.clone(), uuid);
             }
         }
 
         // Iterate edges: only process outgoing to avoid duplicates
-        for key in &keys {
-            let uuid = match index::get_uuid_for_key(db, key) {
-                Ok(Some(u)) => u,
-                _ => continue,
-            };
-            let edges = match index::edges_for_node(db, &uuid) {
+        for (key, uuid) in &key_to_uuid {
+            let edges = match index::edges_for_node(db, uuid) {
                 Ok(e) => e,
                 Err(_) => continue,
             };
             for (other_uuid, strength, rel_type_byte, is_outgoing) in edges {
-                if !is_outgoing { continue; } // only process outgoing
+                if !is_outgoing { continue; }
                 let target_key = match uuid_to_key.get(&other_uuid) {
                     Some(k) => k,
-                    None => continue, // orphan edge
+                    None => continue,
                 };
-                let rel_type = RelationType::from_u8(rel_type_byte);
-                f(key, target_key, strength, rel_type);
+                f(key, target_key, strength, RelationType::from_u8(rel_type_byte));
             }
         }
     }

src/subconscious/digest.rs

@@ -176,12 +176,6 @@ pub fn apply_digest_links(store: &mut Store, links: &[DigestLink]) -> (usize, us
 
         if source == target { skipped += 1; continue; }
 
-        // Check if link already exists
-        let exists = store.relations.iter().any(|r|
-            r.source_key == source && r.target_key == target && !r.deleted
-        );
-        if exists { skipped += 1; continue; }
-
         let source_uuid = match store.get_node(&source).ok().flatten() {
             Some(n) => n.uuid,
             None => { skipped += 1; continue; }
@@ -191,6 +185,12 @@ pub fn apply_digest_links(store: &mut Store, links: &[DigestLink]) -> (usize, us
             None => { skipped += 1; continue; }
         };
 
+        // Check if link already exists via index
+        let exists = store.neighbors(&source).ok()
+            .map(|n| n.iter().any(|(k, _)| k == &target))
+            .unwrap_or(false);
+        if exists { skipped += 1; continue; }
+
         let rel = new_relation(
             source_uuid, target_uuid,
             store::RelationType::Link,